Definitely not. Like I said, this was only her moment in the sense that she's never been allowed to be powerful onscreen in the show unless she was Phoenix. This "moment" was making up for the past few decades since the show started with her being wasted.
Her real time is coming. Dark Phoenix has been in pretty much all the opening themes so far. Storm and Magneto were confirmed as omega-level mutants, but Jean hasn't so far. Don't forget who beats Bastion in X-Men: Next Dimension.
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They may not have been sure but the Phoenix Force most definitely would have. It doesnt make sense for the PF to have been duped by some Sinister clone. Really the only time for the switch to have worked would it to have occurred after the second wedding when Sinister kidnapped Jean in season 4. Im with whitecrown on there. Jean was barely in season 5 so it wouldnt mess with too much of the OG series if they go that route